For clarity - you mention a 1" shim between deeps plus a 6" dry sugar shim, and then a 6" box of shavings on top of that - is that correct? If you have a sugar brick between the deeps that could be a big problem, keeping the bees from moving up into the upper deep as the winter progressed. Even a 1" open space between the deeps could keep them from moving up in cold weather, such that they would be trapped below and eventually starve.
Are there dead bees in the hive, or are they all gone? If they are all gone, or there are only a few bees, I would suspect mites. If they are there, where in the hive are they (upper deep/lower deep/between the two)? Are they in a cluster encompassing a few frames, or spread around the hive? Are there food stores near where they are?